X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Liquid Diffusion
pH 6.7
Temperature 298.0
Details Protein crystallized from 2.2M Sodium/Potassium Phosphate, batch method, pH 6.7, LIQUID DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.17 α = 90
b = 53.17 β = 90
c = 192.98 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5412 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.2 36.9 99.7 0.121 -- -- 11.05 -- 14858 -- -- 53.07
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.2 2.28 99.9 0.455 -- 4.5 13.24 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
FOURIER SYNTHESIS 2.2 36.9 -- 1.33 -- 13249 1477 99.45 -- 0.2142 0.2101 0.2499 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.2 2.24 -- 139 1241 0.2521 0.3203 -- 100.0
X Ray Diffraction 2.24 2.2831 -- 137 1300 0.2263 0.2767 -- 100.0
X Ray Diffraction 2.2831 2.3297 -- 143 1259 0.2336 0.298 -- 100.0
X Ray Diffraction 2.3297 2.3803 -- 140 1253 0.228 0.3041 -- 100.0
X Ray Diffraction 2.3803 2.4357 -- 137 1305 0.2145 0.3108 -- 100.0
X Ray Diffraction 2.4357 2.4966 -- 134 1252 0.2409 0.2976 -- 100.0
X Ray Diffraction 2.4966 2.5641 -- 143 1260 0.2336 0.3357 -- 100.0
X Ray Diffraction 2.5641 2.6395 -- 141 1282 0.2503 0.362 -- 100.0
X Ray Diffraction 2.6395 2.7247 -- 138 1256 0.2291 0.3151 -- 100.0
X Ray Diffraction 2.7247 2.822 -- 146 1279 0.2386 0.2818 -- 100.0
X Ray Diffraction 2.822 2.935 -- 142 1270 0.2481 0.3586 -- 100.0
X Ray Diffraction 2.935 3.0685 -- 142 1266 0.245 0.2862 -- 100.0
X Ray Diffraction 3.0685 3.2302 -- 135 1284 0.2569 0.342 -- 100.0
X Ray Diffraction 3.2302 3.4324 -- 145 1263 0.2305 0.2749 -- 100.0
X Ray Diffraction 3.4324 3.6972 -- 142 1269 0.2 0.2691 -- 100.0
X Ray Diffraction 3.6972 4.0688 -- 141 1269 0.1912 0.2062 -- 100.0
X Ray Diffraction 4.0688 4.6566 -- 141 1237 0.1688 0.2193 -- 98.0
X Ray Diffraction 4.6566 5.8631 -- 140 1231 0.1978 0.2159 -- 96.0
X Ray Diffraction 5.8631 36.9098 -- 136 1225 0.1976 0.1933 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.4701
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_angle_d 1.184
f_dihedral_angle_d 14.49
f_bond_d 0.023
f_chiral_restr 0.069
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2193
Nucleic Acid Atoms 0
Heterogen Atoms 90
Solvent Atoms 60

Software

Software
Software Name Purpose
d*TREK data scaling
d*TREK data reduction version: 9.9.9.4 W9RSSI
PHENIX refinement version: 1.8.2_1309
PDB_EXTRACT data extraction version: 3.11